Yeah, this can be a frightening concept to begin with, I Use a couple of methods to help me,

Firstly, remembering E A D G B E is easy, so i learnt the notes across the third fret
___A
GCF_DG (The A is on the second fret)

Then the fith fret ADGCEA (You probably know most of them anyway)

I continued this on each of the marked frets allong the fretboard (Forget about the ninth fret, learn all the tenth frets instead) DGCFAD

This I find helps because when you arn't sure of a note, there is always one nearby to use as reference.